I typically create a trigger for lookup tables that convert items inserted in a consistant way. I'm betting the UPPERCASE DB has a before insert trigger on that table. Check out the view: user_triggers.

My Question is here. Are you using two diffent copies of application or the application is replicated.Look
1. If you use exactly same copy of applications over two sites t hen it si probabilly on the server side.
2. In the situtation you provied I believe that the it is change in application code.

At one site it is happening.

Insert into table(column1) values (upper(value));

and 2nd site it is:
Insert into table(column1) values (lower(value));
or
Insert into table(column1) values (value);

I think there was a trigger in your DB previously for converting the column values into UPPER CASE. The trigger can be made here. For a example, for converting ENAME (Employee Name) column to upper case in EMP table the trigger will be,

create or replace trigger trg_upper_emp_ename before insert or update of ename on emp for each row
begin
:new.ename := upper(:new.ename);
end;
/

You can create a trigger like this in your DB. Also update all the existing values of the column in the DB.
update emp set ename = UPPER(ename);

Using SQL Scripts we can save all the SQL queries as files that we use very frequently on our database later point of time. This is one of the feature present under SQL Workshop in Oracle Application Express.

Shell script to create broker configuration file using current broker Configuration, solely for purpose of backup on Linux.
Script may need to be modified depending on OS-installation.
Please deploy and verify the script in a test environment.